# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 13:47:54 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-fluoro-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(O)c(F)c1)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 YOF  YOF  '3-fluoro-L-tyrosine      '  L-peptide  23  14  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_YOF
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 YOF  N    N  NH2    0  -0.796  37.8099  28.7513  16.4117
 YOF  CA   C  CH1    0  -0.175  36.6086  28.4583  17.1811
 YOF  C    C  C      0   0.409  36.6103  29.3042  18.4752
 YOF  O    O  O      0  -0.611  37.6525  29.2324  19.1617
 YOF  OXT  O  OC    -1  -0.602  35.5840  29.9593  18.7350
 YOF  CB   C  CH2    0  -0.526  36.4849  26.9624  17.5354
 YOF  CG   C  CR6    0   0.130  35.2389  26.6203  18.2979
 YOF  CD1  C  CR16   0  -0.467  34.0100  26.5369  17.6418
 YOF  CD2  C  CR16   0  -0.308  35.2547  26.4069  19.6711
 YOF  CE1  C  CR6    0   0.480  32.8631  26.2505  18.3460
 YOF  CE2  C  CR16   0  -0.356  34.0927  26.1132  20.3744
 YOF  CZ   C  CR6    0   0.184  32.8707  26.0271  19.7203
 YOF  OH   O  OH1    0  -0.625  31.6996  25.7410  20.3215
 YOF  F    F  F      0  -0.319  31.6869  26.1742  17.6978
 YOF  H    H  HNH2   0   0.332  37.9063  28.0829  15.6559
 YOF  H2   H  HNH2   0   0.326  38.6099  28.6110  17.0175
 YOF  HA   H  HCH1   0   0.198  35.7397  28.7353  16.5758
 YOF  HB2  H  HCH2   0   0.233  36.5127  26.3872  16.6046
 YOF  HB3  H  HCH2   0   0.229  37.3653  26.6699  18.1135
 YOF  HD1  H  HCR6   0   0.266  33.9444  26.6924  16.5709
 YOF  HD2  H  HCR6   0   0.248  36.1909  26.4695  20.2122
 YOF  HE2  H  HCR6   0   0.274  34.1376  25.9457  21.4447
 YOF  HH   H  HOH1   0   0.476  31.8373  25.6065  21.2661

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 YOF  N    CA   single    1.458  0.019  1.458
 YOF  N    H    single    0.860  0.020  0.860
 YOF  N    H2   single    0.890  0.020  1.040
 YOF  CA   C    single    1.525  0.021  1.525
 YOF  CA   CB   single    1.530  0.020  1.530
 YOF  CA   HA   single    0.970  0.020  0.970
 YOF  C    O    deloc     1.231  0.020  1.231
 YOF  C    OXT  deloc     1.245  0.020  1.245
 YOF  CB   CG   single    1.500  0.020  1.500
 YOF  CB   HB2  single    0.970  0.020  1.090
 YOF  CB   HB3  single    0.970  0.020  1.090
 YOF  CG   CD1  aromatic  1.396  0.020  1.396
 YOF  CG   CD2  aromatic  1.390  0.020  1.390
 YOF  CD1  CE1  aromatic  1.376  0.020  1.376
 YOF  CD1  HD1  single    0.930  0.020  1.080
 YOF  CD2  CE2  aromatic  1.390  0.020  1.390
 YOF  CD2  HD2  single    0.930  0.020  1.080
 YOF  CE1  CZ   aromatic  1.392  0.020  1.392
 YOF  CE1  F    single    1.345  0.020  1.345
 YOF  CE2  CZ   aromatic  1.389  0.020  1.389
 YOF  CE2  HE2  single    0.930  0.020  1.080
 YOF  CZ   OH   single    1.347  0.020  1.347
 YOF  OH   HH   single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 YOF  H2   N    H    106.23  3.000
 YOF  H2   N    CA   107.91  3.000
 YOF  H    N    CA   114.00  3.000
 YOF  HA   CA   CB   109.00  3.000
 YOF  HA   CA   C    109.00  3.000
 YOF  CB   CA   C    110.10  1.900
 YOF  HA   CA   N    110.00  3.000
 YOF  CB   CA   N    110.50  1.700
 YOF  C    CA   N    111.00  2.800
 YOF  OXT  C    O    127.08  3.000
 YOF  OXT  C    CA   117.50  3.000
 YOF  O    C    CA   120.80  1.700
 YOF  HB3  CB   HB2  106.77  3.000
 YOF  HB3  CB   CG   109.82  3.000
 YOF  HB2  CB   CG   109.49  3.000
 YOF  HB3  CB   CA   108.44  3.000
 YOF  HB2  CB   CA   108.20  3.000
 YOF  CG   CB   CA   113.86  3.000
 YOF  CD2  CG   CD1  117.73  3.000
 YOF  CD2  CG   CB   121.86  3.000
 YOF  CD1  CG   CB   120.40  3.000
 YOF  HD1  CD1  CE1  119.01  3.000
 YOF  HD1  CD1  CG   120.61  3.000
 YOF  CE1  CD1  CG   120.39  3.000
 YOF  HD2  CD2  CE2  118.83  3.000
 YOF  HD2  CD2  CG   119.64  3.000
 YOF  CE2  CD2  CG   121.54  3.000
 YOF  F    CE1  CZ   118.12  3.000
 YOF  F    CE1  CD1  119.61  3.000
 YOF  CZ   CE1  CD1  122.27  3.000
 YOF  HE2  CE2  CZ   119.46  3.000
 YOF  HE2  CE2  CD2  119.84  3.000
 YOF  CZ   CE2  CD2  120.70  3.000
 YOF  OH   CZ   CE2  124.60  3.000
 YOF  OH   CZ   CE1  118.02  3.000
 YOF  CE2  CZ   CE1  117.37  3.000
 YOF  HH   OH   CZ   110.05  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 YOF  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 YOF  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 YOF  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 YOF  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 YOF  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 YOF  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 YOF  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 YOF  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 YOF  CONST_09  F    CE1  CD1  CG   180.00   0.0  0
 YOF  CONST_10  OH   CZ   CE1  CD1  180.00   0.0  0
 YOF  CONST_11  OH   CZ   CE2  CD2  180.00   0.0  0
 YOF  CONST_12  F    CE1  CZ   CE2  180.00   0.0  0
 YOF  CONST_13  HE2  CE2  CD2  CG   180.00   0.0  0
 YOF  CONST_14  HD2  CD2  CG   CD1  180.00   0.0  0
 YOF  CONST_15  HD1  CD1  CG   CD2  180.00   0.0  0
 YOF  Var_01    CD1  CG   CB   CA    76.51  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 YOF  chir_01  CA  N  C  CB  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 YOF  plan-1  CB   0.020
 YOF  plan-1  CG   0.020
 YOF  plan-1  CD1  0.020
 YOF  plan-1  CD2  0.020
 YOF  plan-1  CE1  0.020
 YOF  plan-1  CE2  0.020
 YOF  plan-1  CZ   0.020
 YOF  plan-1  OH   0.020
 YOF  plan-1  F    0.020
 YOF  plan-1  HD1  0.020
 YOF  plan-1  HD2  0.020
 YOF  plan-1  HE2  0.020
 YOF  plan-2  CA   0.020
 YOF  plan-2  C    0.020
 YOF  plan-2  O    0.020
 YOF  plan-2  OXT  0.020

